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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure of coxsackievirus cloverleaf RNA and 3C pro dimer establishes the RNA-binding mechanism of enterovirus protease 3C pro

In positive-strand RNA viruses, the genome serves as a template for both protein translation and negative-strand RNA synthesis. Enteroviruses use the cloverleaf RNA structure at the 5′ end of the genome to balance these two processes. Cloverleaf acts as a promoter for RNA synthesis and forms a complex with viral 3CD protein, the precursor to 3C pro protease, and 3D pol polymerase. The interaction between cloverleaf and 3CD is mediated by the 3C pro domain, yet how 3C pro promotes specific RNA-binding is not clear. We report the structure of coxsackievirus cloverleaf RNA-3C pro complex, wherein two 3C pro molecules interact with cloverleaf stem-loop D. 3C pro dimer mainly recognizes the shape of the dsRNA helix through symmetric interactions, suggesting that 3C pro is a previously undiscovered type of RNA binding protein. We show that 3CD protein also dimerizes on cloverleaf RNA and binds the RNA with higher affinity than 3C pro . The structure provides insight into the RNA-binding mechanism of 3C pro or 3CD with other cis-acting replication elements.

Science & Technology - Other Topics↗
DOE OSTI2025

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Lignin contains a variety of interunit linkages, leading to a range of potential decomposition products that can be used as carbon and energy sources by microbes. β-O-4 linkages are the most common in native lignin, and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from β-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains of Novosphingobium aromaticivorans with improved catabolism of a model aromatic dimer containing a β-O-4 linkage, guaiacylglycerol-β-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide polymorphism in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, β-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Dimer description of the SU(4) antiferromagnet on the triangular lattice

In systems with many local degrees of freedom, high-symmetry points in the phase diagram can provide an important starting point for the investigation of their properties throughout the phase diagram. In systems with both spin and orbital (or valley) degrees of freedom such a starting point gives rise to SU(4)-symmetric models. Here we consider SU(4)-symmetric "spin" models, corresponding to Mott phases at half-filling, i.e. the six-dimensional representation of SU(4). This may be relevant to twisted multilayer graphene. In particular, we study the SU(4) antiferromagnetic "Heisenberg" model on the triangular lattice, both in the classical limit and in the quantum regime. Carrying out a numerical study using the density matrix renormalization group (DMRG), we argue that the ground state is non-magnetic. We then derive a dimer expansion of the SU(4) spin model. An exact diagonalization (ED) study of the effective dimer model suggests that the ground state breaks translation invariance, forming a valence bond solid (VBS) with a 12-site unit cell. Finally, we consider the effect of SU(4)-symmetry breaking interactions due to Hund's coupling, and argue for a possible phase transition between a VBS and a magnetically ordered state.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

1,3-Dimethyl-2,3-dihydrobenzo[ d ]imidazoles, 1H , and 1,1',3,3'-tetramethyl-2,2',3,3'-tetrahydro-2,2'-bibenzo[ d ]imidazoles, 1 2 , are of interest as n-dopants for organic electron-transport materials. Salts of 2-(4-(dimethylamino)phenyl)-4,7-dimethoxy-, 2-cyclohexyl-4,7-dimethoxy-, and 2-(5-(dimethylamino)thiophen-2-yl)benzo[ d ]imidazolium ( 1g–i + , respectively) have been synthesized and reduced with NaBH 4 to 1gH , 1hH , and 1iH , and with Na:Hg to 1g 2 and 1h 2 . Their electrochemistry and reactivity were compared to those derived from 2-(4-(dimethylamino)phenyl)- ( 1b + ) and 2-cyclohexylbenzo[ d ]imidazolium ( 1e + ) salts. E ( 1 + / 1 • ) values for 2-aryl species are less reducing than for 2-alkyl analogues, i.e., the radicals are stabilized more by aryl groups than the cations, while 4,7-dimethoxy substitution leads to more reducing E ( 1 + / 1 • ) values, as well as cathodic shifts in E ( 1 2 •+ / 1 2 ) and E ( 1H •+ / 1H ) values. Both the use of 3,4-dimethoxy and 2-aryl substituents accelerates the reaction of the 1H species with PC 61 BM. Because 2-aryl groups stabilize radicals, 1b 2 and 1g 2 exhibit weaker bonds than 1e 2 and 1h 2 and thus react with 6,13-bis(triisopropylsilylethynyl)pentacene ( VII ) via a “cleavage-first” pathway, while 1e 2 and 1h 2 react only via “electron-transfer-first”. 1h 2 exhibits the most cathodic E ( 1 2 •+ / 1 2 ) value of the dimers considered here and, therefore, reacts more rapidly than any of the other dimers with VII via “electron-transfer-first”. Crystal structures show rather long central C–C bonds for 1b 2 (1.5899(11) and 1.6194(8) Å) and 1h 2 (1.6299(13) Å).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1978

Laser excited fluorescence in the cesium-xenon excimer and the cesium dimer

Argon ion laser lines are used to excite fluorescence in a mixture of cesium and xenon. Excimer band fluorescence is observed at higher pressures (about 1 atm) while at lower pressures (several torr) a diffuse fluorescence due to the cesium dimer is observed whose character changes with exciting wavelength. The excimer fluorescence is shown to be directly related to the location of the exciting wavelength within previously measured Cs/Xe line shapes. This fact suggests that the excimer systems may be efficiently pumped through these line shapes. Qualitative energy-level schemes are proposed to explain the observations in both the excimer and dimer systems.

Exton, R. J.↗
NASA NTRS1981

Electron-temperature dependence of dissociative recombination of electrons with N2/+/.N2 dimer ions

The variation with electron temperature of the dissociative recombination of electrons with N2(+).N2 dimer ions is investigated in light of the importance of such ions in the lower ionosphere and in laser plasmas. Dissociative recombination coefficients were determined by means of a microwave afterglow mass spectrometer technique for electron temperatures from 300-5600 K and an ion and neutral temperature of 300 K. The recombination coefficient is found to be proportional to the -0.41 power of the electron temperature in this range, similar to that observed for the CO(+).CO dimer ion and consistent with the expected energy dependence for a fast dissociative process.

Whitaker, M.↗
NASA NTRS1982

Theory of metal atom-water interactions and alkali halide dimers

Theoretical studies of the interactions of metal atoms with water and some of its isoelectronic analogs, and of the properties of alkali halides and their aggregates are discussed. Results are presented of ab initio calculations of the heats of reaction of the metal-water adducts and hydroxyhydrides of Li, Be, B, Na, Mg, and Al, and of the bond lengths and angles an; the heats of reaction for the insertion of Al into HF, H2O, NH3, H2S and CH3OH, and Be and Mg into H2O. Calculations of the electron affinities and dipole moments and polarizabilities of selected gas phase alkali halide monomers and dimers are discussed, with particular attention given to results of calculations of the polarizability of LiF taking into account electron correlation effects, and the polarizability of the dimer (LiF)2.

Jordan, K. D.↗
NASA NTRS1984

Hydrogen dimer structures in the far-infrared spectra of Jupiter and Saturn

On the basis of a spectral line shape computation and radiative transfer calculations, it is shown that the unexplained, diminutive structures seen in the Voyager IRIS Jovian spectra near the hydrogen S0(0) and S0(1) rotational frequencies are due to bound-free transitions involving hydrogen dimers. The absorption intensities of these transitions, as well as of the collision-induced background, are given. These dimer structures may possibly prove to be useful for determining the helium/hydrogen ratio and the para-hydrogen fraction in the atmospheres of the outer planets.

Frommhold, L.↗
NASA NTRS1985

Theoretical studies of transition metal dimers

The CASSCF approach was used to perform the MCSCF calculations for a number of transition metal dimers, including the Sc2, Ti2, Cr2, Cu2, TiV, Y2, Nb2, and Mo2 molecules; in addition, CASSCF/CI calculations were carried out for Sc2, Ti2, Cu2, and Y2. The CASSCF procedure is shown to provide a consistent set of calculations for these molecules, from which trends and a simple qualitative picture of the electronic structure may be derived. In particular, the calculations confirmed the ground states of the Sc2 and the TiV, and led to predictions for other molecules in this series. In addition to specific predictions, the study provides a simple qualitative picture of the bonding in these dimers.

Walch, Stephen P.↗
NASA NTRS1989

High-resolution near-infrared spectroscopy of water dimer

High-resolution near-infrared spectra are reported for all of the O-H stretch vibrational bands of the water dimer. The four O-H vibrations are characterized as essentially independent proton-donor or proton-acceptor motions. In addition to the rotational and vibrational information contained in these spectra, details are obtained concerning the internal tunneling dynamics in both the ground and excited vibrational states. These results show that, for tunneling motions which involve the interchange of the proton donor and acceptor molecules, the associated frequencies decrease substantially due to vibrational excitation. The predissociation lifetimes for the various states of the dimer are determined from linewidth measurements. These results clearly show that the predissociation dynamics is strongly dependent on the tunneling states, as well as the Ka quantum number, indicating that the internal tunneling dynamics plays an important role in determining the dissociation rate in this complex.

Huang, Z. S.↗
NASA NTRS1992

On the inclusion of the hydrogen dimer in the analysis of Voyager IRIS spectra

Empirical formulas are fitted to existing theoretical absorption spectra of H2-H2 pairs in the far-infrared allowing the inclusion of dimer absorption, parameterized with the height dependence of the para-hydrogen profile, in the calculations. Comparison between synthetic and Voyager IRIS spectra shows that once the dimer absorption is included it is now possible to reproduce the hydrogen portion of the IRIS spectrum to within the precision of the measurements.

Carlson, Barbara E.↗
NASA NTRS1993

Hydrogen bonding in the benzene-ammonia dimer

High-resolution optical and microwave spectra of the gas-phase benzene-ammonia dimer were obtained, showing that the ammonia molecule resides above the benzene plane and undergoes free, or nearly free, internal rotation. To estimate the binding energy (De) and other global properties of the intermolecular potential, theoretical calculations were performed for the benzene-ammonia dimer, using the Gaussian 92 (Fritsch, 1992) program at the MP2/6-31G** level. The predicted De was found to be at the lowest end of the range commonly accepted for hydrogen bonding and considerably below that of C6H6-H2O, consistent with the gas-phase acidities of ammonia and water. The observed geometry greatly resembles the amino-aromatic interaction found naturally in proteins.

Rodham, David A.↗
NASA NTRS1995

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Karpas, Z.↗
NASA NTRS1995

Absorption cross sections of the ClO dimer

The absorption cross sections of the ClO dimer, ClOOCl, are important to the photochemistry of ozone depletion in the Antarctic. In this work, new measurements were made of the dimer cross sections at 195 K. the results yield somewhat lower values in the long wavelength region, compared to those currently recommended in the NASA data evaluation (JPL 94-26). The corresponding solar photodissociation rates in the Antarctic are reduced by about 40%.

Huder, K. J.↗
DOE OSTI2022

Tuning the Product Distribution of Acetylene Dimerization through Bimetallic Metal–Organic Framework-Supported Nanoporous Systems

Metal-organic frameworks (MOFs) are receiving increased attention due to their well-defined structures that allow the determination of structure-property relationships. MOFs have been used as heterogeneous catalyst supports in a variety of fashions including for confinement of metal nanoparticles, which have demonstrated enhanced resistance to aggregation, a common issue in amorphous metal oxide supports. Cu and In catalysts were installed in the Zr-based MOF NU-907, being confined within the nanoporous structure. The Cu catalyst is known to, under various conditions, either selectively hydrogenate acetylene to ethylene or generate C4 products such as butenes and 1,3-butadiene, an important feedstock for rubber and adhesives. The addition of indium to the Cu catalyst is intended to serve as a promoter to produce C4 products by decreasing the surface coverage of copper while still allowing for C-C coupling. When employed for acetylene dimerization, InCu-NU-907 shows slightly decreased C4 production overall but enhanced 1,3-butadiene production compared to all other catalysts studied herein. These catalysts were thoroughly characterized by a range of techniques to confirm structural integrity and porosity and probe the nature of the interactions of indium with the Cu nanoparticle active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Quantum computation solves a half-century-old enigma: Elusive vibrational states of magnesium dimer found

The high-lying vibrational states of the magnesium dimer (Mg 2 ), which has been recognized as an important system in studies of ultracold and collisional phenomena, have eluded experimental characterization for half a century. Until now, only the first 14 vibrational states of Mg 2 have been experimentally resolved, although it has been suggested that the ground-state potential may support five additional levels. Here, we present highly accurate ab initio potential energy curves based on state-of-the-art coupled-cluster and full configuration interaction computations for the ground and excited electronic states involved in the experimental investigations of Mg 2 . Our ground-state potential unambiguously confirms the existence of 19 vibrational levels, with ~1 cm -1 root mean square deviation between the calculated rovibrational term values and the available experimental and experimentally derived data. Our computations reproduce the latest laser-induced fluorescence spectrum and provide guidance for the experimental detection of the previously unresolved vibrational levels.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase

The ability to sense and respond to environmental cues is essential for adaptation and survival in living organisms. In bacteria, this process is accomplished by multidomain sensor histidine kinases that undergo autophosphorylation in response to specific stimuli, thereby triggering downstream signaling cascades. However, the molecular mechanism of allosteric activation is not fully understood in these important sensor proteins. Here, we report the full-length crystal structure of a blue light photoreceptor LOV histidine kinase (LOV-HK) involved in light-dependent virulence modulation in the pathogenic bacterium Brucella abortus. Joint analyses of dark and light structures determined in different signaling states have shown that LOV-HK transitions from a symmetric dark structure to a highly asymmetric light state. The initial local and subtle structural signal originated in the chromophore-binding LOV domain alters the dimer asymmetry via a coiled-coil rotary switch and helical bending in the helical spine. These amplified structural changes result in enhanced conformational flexibility and large-scale rearrangements that facilitate the phosphoryl transfer reaction in the HK domain.

59 BASIC BIOLOGICAL SCIENCES↗